1SBR

The structure and function of B. subtilis YkoF gene product: the complex with thiamin

1SBR の概要

• エントリーDOI: 10.2210/pdb1sbr/pdb
• 関連するPDBエントリー: 1LXJ 1LXN 1S99
• 分子名称: ykoF, CALCIUM ION, 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM, ... (4 entities in total)
• 機能のキーワード: ykof, thiamin-binding protein, act-domain family, ligand binding protein
• 由来する生物種: Bacillus subtilis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 45629.36

構造登録者

Devedjiev, Y.,Surendranath, Y.,Derewenda, U.,Derewenda, Z.S. (登録日: 2004-02-11, 公開日: 2004-10-05, 最終更新日: 2024-10-30)

主引用文献

Devedjiev, Y.,Surendranath, Y.,Derewenda, U.,Gabrys, A.,Cooper, D.R.,Zhang, R.G.,Lezondra, L.,Joachimiak, A.,Derewenda, Z.S.
The Structure and Ligand Binding Properties of the B.subtilis YkoF Gene Product, a Member of a Novel Family of Thiamin/HMP-binding Proteins
J.Mol.Biol., 343:395-406, 2004

PubMed Abstract: The crystal structure of the Bacillus subtilis YkoF gene product, a protein involved in the hydroxymethyl pyrimidine (HMP) salvage pathway, was solved by the multiwavelength anomalous dispersion (MAD) method and refined with data extending to 1.65 A resolution. The atomic model of the protein shows a homodimeric association of two polypeptide chains, each containing an internal repeat of a ferredoxin-like betaalphabetabetaalphabeta fold, as seen in the ACT and RAM-domains. Each repeat shows a remarkable similarity to two members of the COG0011 domain family, the MTH1187 and YBL001c proteins, the crystal structures of which were recently solved by the Northeast Structural Genomics Consortium. Two YkoF monomers form a tightly associated dimer, in which the amino acid residues forming the interface are conserved among family members. A putative small-ligand binding site was located within each repeat in a position analogous to the serine-binding site of the ACT-domain of the Escherichia coli phosphoglycerate dehydrogenase. Genetic data suggested that this could be a thiamin or HMP-binding site. Calorimetric data confirmed that YkoF binds two thiamin molecules with varying affinities and a thiamine-YkoF complex was obtained by co-crystallization. The atomic model of the complex was refined using data to 2.3 A resolution and revealed a unique H-bonding pattern that constitutes the molecular basis of specificity for the HMP moiety of thiamin.

PubMed: 15451668
DOI: 10.1016/j.jmb.2004.08.037

実験手法

X-RAY DIFFRACTION (2.3 Å)